More than one output for EMBOSS apps

James Bonfield jkb at
Mon Mar 24 13:49:18 UTC 2003

On Mon, Mar 24, 2003 at 12:21:11PM +0000, Peter Rice wrote:
> Several applications have more than one output. Some of the output files 
> are optional, some are more complicated.

This raises a related topic; how we determine what the output files are

For text outputs these are typically (always?) an option and can be set by the 
user. For graphical outputs saved with -graph data the names are just
generated. This has several problems:

1. You can't run emboss in such a manner in a read-only directory. (see below) 

2. The output always overwrites the previous output.

3. There's no way of knowing what files have been generated short of deleting
(regexp) progname[0-9]+\.dat, running the code, and then globbing.

I thought I'd better just check the change log and I see that from 2.7.0
onwards some of these solved (specifically 1, which makes dealing with 2 and 3
easier). So things are getting there :)


James Bonfield (jkb at   Fax: (+44) 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at

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